TABLE 3 .

Estimates of the population recombination rate (ρ), tests of recombination based on homoplasy and linkage disequilibrium, and the proportion of homoplastic SNPs

Lineage	ρ (no. of crossovers/Mbp/generation) on chromosomea								% homoplastic SNPs	phi test P value
	1	2	3	4	5	6	7	Mean
1	8.6*	3.8*	15.1*	1.4	8.5*	10.6*	13.5*	10.57	34.56	0.0000
2	0.0	0.2	0.2*	0.3	0.6	0.5	0.3	0.28	0.09	0.0944
3	0.4*	0.2*	0.0	0.0	0.0	0.0	0.0	0.01	0.47	0.0535
4	0.2	0.2*	0.3	0.4	0.4	0.4	0.4	0.33	0.40	0.0014

^a*, P < 0.05. The phi test assesses pairwise homoplasy. The null hypothesis of no recombination was tested, with the phi test and for ρ, using random permutations of the positions of the SNPs based on the expectation that sites are exchangeable if there is no recombination. For the ρ test, significance was determined from the distribution of maximum composite likelihood values calculated from permuted data.